8-124851782-A-T

Variant names:

• chr8-124851782-A-T
• rs6470289
• ENST00000528090.5:n.327+1829A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528090.5(LINC00964):​n.327+1829A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,012 control chromosomes in the GnomAD database, including 18,216 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18216 hom., cov: 32)
• Consequence: LINC00964 ENST00000528090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 3 publications found

Genes affected

LINC00964 (HGNC:27226): (long intergenic non-protein coding RNA 964)

ENSG00000255491 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375743	NR_188058.1	n.153+5581T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00964	ENST00000528090.5	n.327+1829A>T		intron_variant	Intron 3 of 5	4
ENSG00000255491	ENST00000533496.1	n.154+5581T>A		intron_variant	Intron 1 of 2	4
LINC00964	ENST00000654805.2	n.474+1829A>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73828 AN: 151894 Hom.: 18205 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.486 AC: 73870 AN: 152012 Hom.: 18216 Cov.: 32 AF XY: 0.487 AC XY: 36144 AN XY: 74284

African (AFR) AF: 0.446 AC: 18491 AN: 41458

American (AMR) AF: 0.478 AC: 7300 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3427 AN: 5170

South Asian (SAS) AF: 0.518 AC: 2490 AN: 4810

European-Finnish (FIN) AF: 0.454 AC: 4788 AN: 10546

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33903 AN: 67980

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.349 Hom.: 864

Bravo AF: 0.482

Asia WGS AF: 0.603 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.1
DANN	Benign	0.68
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6470289; hg19: chr8-125864024;